From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Jul 07 2011 - 05:35:07 CDT
I don't know the procedure for NAMD but it can be done with QM/MM calculations using CPMD very fine.
Mit freundlichen Grüßen
Norman Geist.
-----Ursprüngliche Nachricht-----
Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im Auftrag von Francesco Pietra
Gesendet: Donnerstag, 7. Juli 2011 11:53
An: NAMD
Betreff: namd-l: free energy of binding
How could free energy of binding of a small-molecule ligand to a
protein receptor be calculated from namd md trajectories?
Is there a validated specific procedure for namd, or should a
literature method be imitated? For example Åqvist's method:
Åqvist, J., Medina, C., and Samuelsson, J. E. (1994) A new
method for predicting binding affinity in computer-aided drug design.
Protein Eng. 7, 385–391.
thanks for sharing experience on this hot topic
francesco pietra
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